ECMDB: L-Ribulose 5-phosphate (ECMDB20167) (M2MDB001014)

Identification Taxonomy Physical Properties Biological Properties Spectra Concentrations Links References Enzymes (6)XML

Proteins (232)

Record Information

Version

2.0

Creation Date

2012-05-31 14:31:03 -0600

Update Date

2015-06-03 17:19:26 -0600

Secondary Accession Numbers

ECMDB20167

Identification

Name:

L-Ribulose 5-phosphate

Description

L-ribulose 5-phosphate is a member of the chemical class known as Pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms. In Escherichia coli, RpiA catalyzes the interconversion of ribose-5-phosphate and ribulose-5-phosphate and is a key enzyme in the pentose phosphate pathway. (PMID 12182339) Interconversion of D-ribose-5-phosphate (R5P) and D-ribulose-5-phosphate is an important step in the pentose phosphate pathway. (PMID 18640127) A key player in LPS synthesis is the enzyme D-arabinose-5-phosphate isomerase (API), which catalyzes the reversible isomerization of D-ribulose-5-phosphate to D-arabinose-5-phosphate, a precursor of 3-deoxy-D-manno-octulosonate that is an essential residue of the LPS inner core. (PMID 20954237) Dihydroxybutanone phosphate synthase (DS) catalyzes a commitment step in riboflavin biosynthesis where ribulose 5-phosphate is converted to dihydroxybutanone phosphate and formate. (PMID 11053863) Ribose-5-phosphate isomerase A (RpiA) plays an important role in interconverting between ribose-5-phosphate (R5P) and ribulose-5-phosphate in the pentose phosphate pathway and the Calvin cycle. (PMID 19214439)

Structure

MOL SDF PDB SMILES InChI

Synonyms:

5-O-Phosphono-L-erythro-pent-2-ulose
5-O-Phosphono-L-ribulose
L-Erythro-pent-2-ulose 5-(dihydrogen phosphate)
L-erythro-Pent-2-ulose 5-(dihydrogen phosphoric acid)
L-Ribulose 5-(dihydrogen phosphate)
L-Ribulose 5-(dihydrogen phosphoric acid)
L-Ribulose 5-phosphoric acid
L-Ribulose-5-P
Ribulose 5-phosphate
Ribulose 5-phosphoric acid
Ribulose-5-P
Ribulose-5-phosphate
Ribulose-5-phosphoric acid

Chemical Formula:

C₅H₁₁O₈P

Weight:

Average: 230.1098
Monoisotopic: 230.01915384

InChI Key:

FNZLKVNUWIIPSJ-CRCLSJGQSA-N

InChI:

InChI=1S/C5H11O8P/c6-1-3(7)5(9)4(8)2-13-14(10,11)12/h4-6,8-9H,1-2H2,(H2,10,11,12)/t4-,5+/m0/s1

CAS number:

2922-69-2

IUPAC Name:

{[(2S,3S)-2,3,5-trihydroxy-4-oxopentyl]oxy}phosphonic acid

Traditional IUPAC Name:

L-ribulose 5-phosphate

SMILES:

[H][C@](O)(COP(O)(O)=O)[C@]([H])(O)C(=O)CO

Chemical Taxonomy

Description

belongs to the class of organic compounds known as pentose phosphates. These are carbohydrate derivatives containing a pentose substituted by one or more phosphate groups.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Pentose phosphates

Alternative Parents

Substituents

Pentose phosphate
Pentose-5-phosphate
Monosaccharide phosphate
Monoalkyl phosphate
Acyloin
Beta-hydroxy ketone
Organic phosphoric acid derivative
Alkyl phosphate
Phosphoric acid ester
Alpha-hydroxy ketone
Ketone
Secondary alcohol
Polyol
Hydrocarbon derivative
Organic oxide
Carbonyl group
Alcohol
Primary alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

ribulose 5-phosphate (CHEBI:17666 )

Physical Properties

State:

Not Available

Charge:

-2

Melting point:

Not Available

Experimental Properties:

Property	Value	Source

Predicted Properties

Property	Value	Source
Water Solubility	26.1 g/L	ALOGPS
logP	-1.8	ALOGPS
logP	-2.8	ChemAxon
logS	-0.95	ALOGPS
pKa (Strongest Acidic)	1.48	ChemAxon
pKa (Strongest Basic)	-3.3	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	144.52 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	42.47 m³·mol⁻¹	ChemAxon
Polarizability	18.05 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	1	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Biological Properties

Cellular Locations:

Cytoplasm

Reactions:

SMPDB Pathways:

Not Available

KEGG Pathways:

Ascorbate and aldarate metabolism ec00053
Metabolic pathways eco01100
Microbial metabolism in diverse environments ec01120
Pentose and glucuronate interconversions ec00040

EcoCyc Pathways:

L-arabinose degradation I ARABCAT-PWY
L-ascorbate degradation I (bacterial, anaerobic) PWY0-301
L-ascorbate degradation II (bacterial, aerobic) PWY-6961
L-lyxose degradation LYXMET-PWY

Concentrations

Concentration	Strain	Media	Growth Status	Growth System	Temperature	Details
2± 0 uM	W3110	4.0 g/L Na2SO4; 5.36 g/L (NH4)2SO4; 1.0 g/L NH4Cl; 7.3 g/L K2HPO4; 1.8 g/L NaH2PO4 H2O; 12.0 g/L (NH4)2-H-citrate; 4.0 mL/L MgSO4 (1 M); 6.0 mL/L trace element solution; 0.02 g/L thiamine, 20 g/L glucose	Mid Log Phase	Bioreactor, pH controlled, aerated, dilution rate=0.125 L/h	37 oC	Park, C., Park, C., Lee, Y., Lee, S.Y., Oh, H.B., Lee, J. (2011) Determination of the Intracellular Concentration of Metabolites in Escherichia coli Collected during the Exponential and Stationary Growth Phases using Liquid Chromatography-Mass Spectrometry. Bull Korean Chem. Soc. 32: 524-530.
2± 0 uM	W3110	4.0 g/L Na2SO4; 5.36 g/L (NH4)2SO4; 1.0 g/L NH4Cl; 7.3 g/L K2HPO4; 1.8 g/L NaH2PO4 H2O; 12.0 g/L (NH4)2-H-citrate; 4.0 mL/L MgSO4 (1 M); 6.0 mL/L trace element solution; 0.02 g/L thiamine, 20 g/L glucose	Stationary Phase	Bioreactor, pH controlled, aerated	37 oC	Park, C., Park, C., Lee, Y., Lee, S.Y., Oh, H.B., Lee, J. (2011) Determination of the Intracellular Concentration of Metabolites in Escherichia coli Collected during the Exponential and Stationary Growth Phases using Liquid Chromatography-Mass Spectrometry. Bull Korean Chem. Soc. 32: 524-530.

Find out more about how we convert literature concentrations.

Spectra

Spectra:

Spectrum Type	Description	Splash Key
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-01q9-3790000000-2c11b3331f617fcac827	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0btd-9710000000-28813a9eaf50967c87e7	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4i-9200000000-5ba5e3b7a9495a17a555	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-002r-9520000000-88185c13004c51d8fbb9	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9100000000-4b58e89007a1a7f893dd	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-8cddc9cbb874799a0ced	View in MoNA
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer

References

References:

Gourlay, L. J., Sommaruga, S., Nardini, M., Sperandeo, P., Deho, G., Polissi, A., Bolognesi, M. (2010). "Probing the active site of the sugar isomerase domain from E. coli arabinose-5-phosphate isomerase via X-ray crystallography." Protein Sci 19:2430-2439. Pubmed: 20954237
Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
Kim, T. G., Kwon, T. H., Min, K., Dong, M. S., Park, Y. I., Ban, C. (2009). "Crystal structures of substrate and inhibitor complexes of ribose 5-phosphate isomerase A from Vibrio vulnificus YJ016." Mol Cells 27:99-103. Pubmed: 19214439
Liao, D. I., Viitanen, P. V., Jordan, D. B. (2000). "Cloning, expression, purification and crystallization of dihydroxybutanone phosphate synthase from Magnaporthe grisea." Acta Crystallogr D Biol Crystallogr 56:1495-1497. Pubmed: 11053863
Lohrke, S. M., Dery, P. D., Li, W., Reedy, R., Kobayashi, D. Y., Roberts, D. R. (2002). "Mutation of rpiA in Enterobacter cloacae decreases seed and root colonization and biocontrol of damping-off caused by Pythium ultimum on cucumber." Mol Plant Microbe Interact 15:817-825. Pubmed: 12182339
Park, C., Park, C., Lee, Y., Lee, S.Y., Oh, H.B., Lee, J. (2011) Determination of the Intracellular Concentration of Metabolites in Escherichia coli Collected during the Exponential and Stationary Growth Phases using Liquid Chromatography-Mass Spectrometry. Bull Korean Chem. Soc. 32: 524-530.
Roos, A. K., Mariano, S., Kowalinski, E., Salmon, L., Mowbray, S. L. (2008). "D-ribose-5-phosphate isomerase B from Escherichia coli is also a functional D-allose-6-phosphate isomerase, while the Mycobacterium tuberculosis enzyme is not." J Mol Biol 382:667-679. Pubmed: 18640127

Synthesis Reference:

Not Available

Material Safety Data Sheet (MSDS)

Not Available

Links

External Links:

Resource	Link
CHEBI ID	17666
HMDB ID	Not Available
Pubchem Compound ID	439399
Kegg ID	C01101
ChemSpider ID	388516
Wikipedia ID	Not Available
BioCyc ID	L-RIBULOSE-5-P
EcoCyc ID	L-RIBULOSE-5-P
Ligand Expo	HMS

Enzymes

Protein Details

1. L-ribulose-5-phosphate 4-epimerase

General function:: Involved in metal ion binding
Specific function:: L-ribulose 5-phosphate = D-xylulose 5- phosphate
Gene Name:: araD
Uniprot ID:: P08203
Molecular weight:: 25519

Reactions

L-ribulose 5-phosphate = D-xylulose 5-phosphate.

Protein Details

2. Ribulokinase

General function:: Involved in phosphotransferase activity, alcohol group as acceptor
Specific function:: ATP + L(or D)-ribulose = ADP + L(or D)- ribulose 5-phosphate
Gene Name:: araB
Uniprot ID:: P08204
Molecular weight:: 61089

Reactions

ATP + L(or D)-ribulose = ADP + L(or D)-ribulose 5-phosphate.

Protein Details

3. L-ribulose-5-phosphate 4-epimerase sgbE

General function:: Involved in metal ion binding
Specific function:: Catalyzes the isomerization of L-ribulose 5-phosphate to D-xylulose 5-phosphate. May be involved in the utilization of 2,3- diketo-L-gulonate
Gene Name:: sgbE
Uniprot ID:: P37680
Molecular weight:: 25561

Reactions

L-ribulose 5-phosphate = D-xylulose 5-phosphate.

Protein Details

4. L-ribulose-5-phosphate 3-epimerase ulaE

General function:: Involved in intramolecular oxidoreductase activity, interconverting aldoses and ketoses
Specific function:: Catalyzes the isomerization of L-xylulose-5-phosphate to L-ribulose-5-phosphate. Is involved in the anaerobic L-ascorbate utilization
Gene Name:: ulaE
Uniprot ID:: P39305
Molecular weight:: 32006

Reactions

L-ribulose 5-phosphate = L-xylulose 5-phosphate.

Protein Details

5. L-ribulose-5-phosphate 4-epimerase ulaF

General function:: Involved in metal ion binding
Specific function:: Catalyzes the isomerization of L-ribulose 5-phosphate to D-xylulose 5-phosphate. Is involved in the anaerobic L-ascorbate utilization
Gene Name:: ulaF
Uniprot ID:: P39306
Molecular weight:: 25278

Reactions

L-ribulose 5-phosphate = D-xylulose 5-phosphate.

Protein Details

6. predicted L-xylulose 5-phosphate 3-epimerase

General function:: Not Available
Specific function:: Not Available
Gene Name:: yiaR
Uniprot ID:: P37679
Molecular weight:: Not Available

L-Ribulose 5-phosphate (ECMDB20167) (M2MDB001014)

Structure for #<Compound:0x9e8dcb30>

Enzymes

Reactions

Reactions

Reactions

Reactions

Reactions